IT HAS BEEN SOLVED!!!

Thank you so much to everyone for your help, but especially pizzaguy! We checked pin 5 on the amplifier and found it was only 4.5 volts. We then checked the same wire coming right out of the radio connector and it was an even lower 3.5 volts. I snipped the wire coming from the radio and then tested the output separate from the wiring harness, and it reported exactly 12. Sure enough, when I directly connected the cut end to the amplifier harness the radio started playing with no problems! The moment I took the wire away, the radio would cut out exactly as it did before. We cut the amplifier harness and spliced our own equal gauge wire in between the two ends. Now there are no more grounding/shorting issues, and after routing the new wire through and tucking everything back into place the stereo works better than ever! Thank you so much again to everyone for your help! I would have spent hundreds trying to fix this without your valuable input.